Alkynyl-derivatized cap analogs, preparation and uses thereof

ABSTRACT

Alkynyl-derivatized cap analogs, alkynyl-modified capped RNA, 1,4-disubstituted triazole-derivatized capped RNA, methods of preparation, methods of isolation, and uses thereof are provided. The “click” modification facilitates detection and isolation of capped RNAs and the 1,4-disubstituted triazole derivatives formed by the “click” reaction are useful for producing RNA transcripts and encoded protein.

RELATED APPLICATION

This application claims the benefit of U.S. Provisional Application No.61/548,653, filed Oct. 18, 2011, the disclosure of which is specificallyincorporated herein by reference in its entirety.

FIELD

This specification generally relates to RNA cap analogs, methods of useand kits. In particular, cap analogs provided herein permit readydetection and/or isolation of capped RNA transcripts in vitro andtranslation of capped mRNAs in vivo.

BACKGROUND

Eukaryotic mRNAs bear a “cap” structure at their 5′-termini that is wellknown to play an important role in translation. Naturally occurring capstructures consist of a 7-methyl guanosine that is linked via atriphosphate bridge to the 5′-end of the first transcribed nucleotide,resulting in m⁷G(5′)ppp(5′)N, where N is any nucleotide. The mRNA capplays an important role in gene expression. It protects the mRNAs fromdegradation by exonucleases, enables transport of RNAs from the nucleusto the cytoplasm, and participates in assembly of the translationinitiation complex. m⁷G(5′)ppp(5′)G (mCAP) has been used as the primerin transcription with T7 or SP6 RNA polymerase in vitro to obtain RNAshaving a cap structure in their 5′-termini. In vivo, the cap is addedenzymatically. However, over the past 20 years or so, numerous studieshave required the synthesis of proteins in an in vitro translationextract supplemented with in vitro synthesized mRNA. The prevailingmethod for the in vitro synthesis of capped mRNA employs a pre-formeddinucleotide of the form m⁷G(5′)ppp(5′)G as an initiator oftranscription. A disadvantage of using mCAP, a pseudosymmetricaldinucleotide, has always been the propensity of the 3′-OH of either theG or m⁷G (m⁷Guo) moiety to serve as the initiating nucleophile fortranscriptional elongation. This disadvantage was addressed by provisionof modified cap analogs having the 3′-OH group of the m⁷G portion of thecap blocked to prevent transcription from that position.

In the cell, the cap is added in the nucleus and is catalyzed by theenzyme guanylyl transferase. The addition of the cap to the 5′ terminalend of RNA occurs after transcription but immediately aftertranscription initiation so that it is almost impossible to detect. Theterminal nucleoside is always a guanine, and is in the reverseorientation to all the other nucleotides, i.e., 5′ Gppp5′ GpNpNp . . .and the cap contains two nucleotides, connected by a 5′-5′ triphosphatelinkage.

Transcription of RNA usually starts with a nucleoside triphosphate(usually a purine, A or G). When transcription occurs in vitro, ittypically includes a phage RNA polymerase such as T7, T3 or SP6, a DNAtemplate containing a phage polymerase promoter, nucleotides (ATP, GTP,CTP and UTP) and a buffer containing magnesium salt. The 5′ capstructure enhances the translation of mRNA by helping to bind theeukaryotic ribosome and assuring recognition of the proper AUG initiatorcodon. This function may vary with the translation system and with thespecific mRNA being synthesized.

During translation the cap is bound by translation initiation factoreIF4E and the cap-binding complex (CBC) recruits additional initiationfactors. Decapping is catalyzed by proteins dcp1 and dcp2 which competewith eIF4E to bind to the cap. Translation results in amino acids asencoded by the mRNA to join together to form a peptide and occurs asthree processes, initiation, elongation and termination. Initiation ineukaryotes involves attachment of a ribosome which scans the mRNA forthe first methionine codon. Elongation proceeds with the successiveaddition of amino acids until a stop codon is reached, terminatingtranslation.

Capped RNA encoding specific genes can be transfected into eukaryoticcells or microinjected into cells or embryos to study the effect oftranslated product in the cell or embryo. If uncapped RNA is used, theRNA in these experiments is rapidly degraded and the yield of translatedprotein is much reduced.

Capped RNA can also be used to treat disease. Isolated dendritic cellsfrom a patient can be transfected with capped RNA encoding immunogen.The dendritic cells translate the capped RNA into a protein that inducesan immune response against this protein. In a small human study,immunotherapy with dendritic cells loaded with CEA capped RNA was shownto be safe and feasible for pancreatic patients (Morse et al., Int. J.Gastroinstest. Cancer, 32, 1-6, (2002)). It was also noted thatintroducing a single capped RNA species into immature dendritic cellsinduced a specific T-cell response (Heiser et al., J. Clin. Invest.,109, 409-417 (2002)).

Thus, there is a need for mRNA cap analogs to produce capped mRNA invitro.

SUMMARY

Aspects of the present disclosure include a composition comprising analkynyl-derivatized cap analog having the structure: R₃^(7,3′-O-alkynyl)G[5′]p[p]_(n)p[5′]G, R₃^(7,3′-O-alkynyl)G[5′]p[p]_(n)p[5′]A, R₃^(7,2′-O-alkynyl)G[5′]p[p]_(n)p[5′]G, R₃^(7,2′-O-alkynyl)G[5′]p[p]_(n)p[5′]A, or a salt thereof; wherein R₃ isalkyl or arylalkyl; the alkynyl moiety comprises 3-24 carbon atoms, aterminal alkyne, and is optionally substituted; n is 1, 2, or 3; A isadenosine; and G is guanosine. Further embodiments of the disclosureinclude a composition comprising RNA having such a cap analog covalentlybonded thereto.

In certain embodiments, the alkynyl-derivatized cap analog comprises thestructure: m^(7,3′-O-alkynyl)G[5′]ppp[5′]G,m^(7,3′-O-alkynyl)G[5′]ppp[5′]A, m^(7,2′-O-alkynyl)G[5′]ppp[5′]G,m^(7,2′-O-alkynyl)G[5′]ppp[5′]A, or a salt thereof, wherein the alkynylmoiety comprises a terminal alkyne and comprises 3-8 carbon atoms, A isadenosine, and G is guanosine. Further aspects include a compositioncomprising such a compound and a physiologically acceptable carrier, ora composition comprising such a compound covalently bonded to RNA.

Other embodiments of the present disclosure include a compositioncomprising an alkynyl-derivatized cap analog having the structure:

or a salt thereof, wherein at least one of R₁ and R₂ comprisesO(CH₂)_(m)C≡CH and m is 1 to 6, and the other of R₁ and R₂ comprises OHor H; R₃ is alkyl or arylalkyl; and R₄ is absent, H, alkyl or arylalkyl.In an embodiment of the composition, R₂ comprises O(CH₂)_(m)C≡CH and mis 1 to 6, and R₁ comprises OH. In another embodiment of thecomposition, R₁ comprises O(CH₂)_(m)C≡CH and m is 1 to 6, and R₂comprises OH. In aspects of the disclosure, n is 1. In aspects of thedisclosure, m is 1. The alkyne group of R₁ or R₂ is a terminal alkyne.

Such alkynyl-derivatized cap analogs are anti-reverse cap analogs sinceat least one of R₁ and R₂ is derivatized. This modification forces RNApolymerases to initiate transcription with the remaining —OH group inthe G residue of the cap and thus synthesize RNA transcripts cappedexclusively in the correct orientation. Therefore, use of the cap analogprovided herein allows for synthesis of capped RNAs that are 100%functional in contrast to transcription reactions using traditional capanalogs where only half of the cap analog is incorporated in the correctorientation.

In some embodiments, compositions are provided comprising:

or a salt thereof, wherein at least one of R₁ and R₂ comprisesO(CH₂)_(m)C≡CH and m is 1 to 6, and the other of R₁ and R₂ comprises OHor H; R₃ is alkyl or arylalkyl; and R₄ is absent, H, alkyl or arylalkyl.

A further embodiment includes a method of synthesizing analkynyl-derivatized cap analog comprises combining a 2′- or a3′-alkynyl-derivatized m7G diphosphate with imidazole-derivatized GMPunder conditions and for a time to produce an alkynyl-derivatized capanalog.

An aspect of the present disclosure is a method of producing5′-alkynyl-modified capped RNA comprising contacting a nucleic acidsubstrate with a RNA polymerase and an alkynyl-derivatized cap analog asdescribed herein in the presence of nucleotide triphosphates underconditions and for a time to produce 5′-alkynyl-modified capped RNA.5′-Alkynyl-derivatized capped mRNAs are used for protein synthesis inreticulocyte lysates, wheat germ lysates, and other in vitro systems,for example.

Isolation and/or detection of such a capped RNA is achieved by a methodcomprising contacting the alkynyl-modified capped RNA with anazide-derivatized moiety to form a 1,4-disubstitutedtriazole-derivatized capped RNA. In an embodiment, the azide-derivatizedmoiety comprises a detectable moiety and the detectable moiety comprisesa reporter molecule, biotin, or a peptide.

In one embodiment, a method comprises contacting a 1,4-disubstitutedtriazole-derivatized capped RNA with a solid support having bindingaffinity and specificity for the detectable moiety. When the detectablemoiety comprises biotin and the solid support comprising avidin orstreptavidin, for example, detection and/or isolation is achieved.

An aspect of the disclosure is a method of separating5′-alkynyl-modified capped RNA from uncapped RNA in a sample, comprisingcontacting the sample with a solid support having an azide-derivatizedcleavable linker bound thereto under conditions and for a time toproduce a 1,4-disubstituted triazole-derivatized capped RNA-solidsupport conjugate; separating the conjugate from uncapped RNA; and,cleaving the 1,4-disubstituted triazole-derivatized capped RNA from thesolid support, thereby separating the alkynyl-modified capped RNA fromuncapped RNA. In some embodiments, the method includes a step offiltration and/or ethanol precipitation. In some embodiments, thecleavable linker comprises a disulfide linkage.

Aspects of a solid support for use in the present disclosure includecompositions comprising a solid support having a cleavable linkerattached thereto and having a terminal azido group for use in “click”chemical reactions. Such compositions, in some embodiments, comprise,for example,

Further embodiments of the present disclosure include a kit for cappingan RNA transcript comprising an alkynyl-derivatized cap analog asdescribed herein; nucleotide triphosphate molecules; and a RNApolymerase. Such kits may further include an azide-derivatized solidsupport, a ribonuclease inhibitor, or a polymerase buffer, for example.

1,4-Disubstituted triazole-derivatized capped RNA can be microinjectedor transfected into cells or organisms for in vivo studies. Accordingly,as aspect of the disclosure is a biological cell comprising a1,4-disubstituted triazole-derivatized capped RNA.

In a further aspect of the disclosure, a method of introducing anexogenous protein into a subject is provided, the method comprisingtransfecting the subject with a 1,4-disubstituted triazole-derivatizedcapped mRNA encoding the exogenous protein; and allowing intracellulartranslation to produce the exogenous protein. In an embodiment in whichthe subject is responsive to immunotherapy, the exogenous protein may bean immunogen. In the case where the subject is a cell, the cell may bean antigen presenting cell (APC).

Other aspects include a method for treatment of disease of a subject,comprising providing to the subject one or more mRNAs comprising a1,4-disubstituted triazole-derivatized cap analog wherein the mRNAencodes a protein that treats the disease. In some embodiments, the mRNAcomprising a 1,4-disubstituted triazole-derivatized cap analog iscontained within a cell and the cell is an antigen presenting cell(APC). In some embodiments, the APC is a dendritic cell, a macrophage, aB cell or a T cell. In some embodiments, the mRNAs comprising a1,4-disubstituted triazole-derivatized cap analog is introduced into thecell by transfection.

Cap analogs and capped RNA as provided herein are also useful for RNAsplicing and for situations in which the stability of RNA is a factor.

BRIEF DESCRIPTION OF THE DRAWINGS

The skilled artisan will understand that the drawings, described below,are for illustration purposes only. The drawings are not intended tolimit the scope of the present teachings in any way.

FIG. 1A-FIG. 1L provide structures of alkynyl-modified cap analogs. FIG.1A-FIG. 1F depict 2′-modified structures while FIG. 1G-FIG. 1L depict3′-modified structures.

FIG. 2 provides a synthetic scheme for producingm^(7,3′-O-propargyl)GpppG7, an alkynyl-modified cap analog.

FIG. 3 provides a general scheme for coupling a RNA bearing analkyne-modified cap analog to an entity bearing an azide group using“click” chemistry.

FIG. 4 provides a flow chart for in vitro transcription in the presenceof an alkynyl-modified cap analog, coupling via “click” chemistry to anazide-derivatized solid support and isolation of capped mRNA.

FIG. 5A provides a reaction scheme for coupling mRNA 7 a bearing alkynylcap analog 7 with azide-derivatized solid-support 10 a to form reactionproduct 11 a, which reaction product is cleaved by DTT to provide cappedmRNA 12 a.

FIG. 5B provides a reaction scheme for coupling analog 7 a withazide-derivatized solid support 10 b to form reaction product 11 b,which reaction product is cleaved by DTT to provide capped mRNA 12 b.

FIG. 6 provides data on the translational efficiency of mRNA forluciferase, the mRNA containing a mixture of standard capped mRNA andalkynyl-modified capped mRNA 7 a.

FIG. 7 provides a scheme for coupling alkynyl-modified capped mRNA 7 awith an azido S—S-Biotin conjugate 13 to form streptavidin-detectablemRNA 14.

FIG. 8A and FIG. 8B provide schemes for preparation of solid-supports 10a and 10 b

DETAILED DESCRIPTION

The present application provides methods and compositions related to capanalogs for use in transcription, for use in detection and isolation ofcapped RNA, for use of resultant isolated RNA in translation both invitro and in vivo. Also included are methods of using the resultantisolated RNA in research and treatment of disease. Thealkynyl-derivatized cap analogs provided herein have the advantage ofonly being incorporated in transcription capping reactions in theforward direction.

In the examples provided below, the effect of the 3′-O-propargylsubstitution on the cap analog has been evaluated with respect to its invitro transcription by using T7 RNA polymerase, capping efficiency andtranslational activity. The gel shift assay indicated that the standardcap analog, m7GppG has a capping efficiency of 73% and thealkynyl-modified cap has a capping efficiency of 60%. The cappingefficiency experiment clearly demonstrated that the alkynyl-modified capanalog was a substrate for T7 RNA polymerase. The results in theexamples show that the mRNA poly(A) capped with 3′-O-propargylsubstituted cap analog (the alkynyl-modified cap analog) was translated3.1 fold more efficiently than the mRNA capped with the standard capanalog (m7GppG). The examples also provide methods for usingsolid-supported “click” chemistry to isolate mRNA that is 100% capped(e.g., contains no uncapped mRNA).

In an embodiment, alkynyl-derivatized capped RNA is detected and/orisolated using “click” technology in which a copper-catalyzed covalentreaction is used to attach the capped RNA to an azide-derivatizedreporter moiety to form a 1,4-disubstituted triazole-derivatized cappedRNA-reporter conjugate. The reporter moiety can be used to detect and/orisolate the capped mRNA from uncapped mRNA.

In another embodiment, alkynyl-derivatized capped RNA is isolated using“click” technology in which a copper-catalyzed covalent reaction is usedto attach the capped RNA to an azide-derivatized solid support to form a1,4-disubstituted triazole-derivatized capped RNA-solid supportconjugate. This allows for isolation of capped mRNA from uncapped RNA.Subsequent cleavage from the solid support, for example, when thealkynyl group or the azide moiety contains a cleavable linker, yieldsderivatized RNA that can be separated from the solid support.

The use of “or” means “and/or” unless stated otherwise or where the useof “and/or” is clearly inappropriate. The use of “a” means “one or more”unless stated otherwise or where the use of “one or more” is clearlyinappropriate. The use of “comprise,” “comprises,” “comprising,”“include,” “includes,” and “including” are interchangeable and notintended to be limiting.

The term “azido” and “azide” are interchangeable and refer to a chemicalcompound that contains the group N₃.

The term “alkynyl” or “alkyne” are interchangeable and refer to ahydrocarbon having at least one terminal triple bond, i.e., thestructure (CH₂)_(m)C≡CH where m is 1 to 22, or 1, 2, 3, 4, 5, 6, 7, 8,9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, or 22. In particular,m is 1, 2, 3, 4, 5, or 6, or m is 1-6, or 1-10, or 1-12, for example.The term “alkynyl” may refer to a branched or an unbranched hydrocarbongroup, or a substituted hydrocarbon chain, or as having furtherunsaturated bonds therein. In some embodiments, the alkynyl isn-propynyl, isopropynyl, n-butynyl, isobutynyl, t-butynyl, octynyl,decynyl and the like. The term “lower alkynyl” intends an alkynyl groupof three to eight carbon atoms.

The term “moiety” and “group” are used interchangeably to refer to aportion of a molecule, typically having a particular functional orstructural feature, e.g. a linking group (a portion of a moleculeconnecting two other portions of the molecule), or an ethyl moiety (aportion of a molecule with a structure closely related to ethane).

The terms “click” or “click chemistry,” as used herein, refer to theHuisgen cycloaddition or the 1,3-dipolar cycloaddition between an azideand a terminal alkyne to form a 1,2,4-triazole.

The term “ARCA” or anti-reverse cap analog refers to a modified capanalog in which either the 3′-OH group or the 2′-OH group of the m⁷G ismodified. This modification forces RNA polymerases to initiatetranscription with the remaining —OH group in the G residue of the capand thus synthesize RNA transcripts capped exclusively in the correctorientation. Therefore, use of the cap analog provided herein allows forsynthesis of capped RNAs that are 100% functional in contrast totranscription reactions using traditional cap analogs where only half ofthe cap analog is incorporated in the correct orientation. Capped mRNAsprovided herein are used for protein synthesis in reticulocyte lysates,wheat germ lysates, and other in vitro systems, or can be microinjectedor transfected into cells or organisms for in vivo studies. They canalso be used in RNA splicing and stability studies.

An alkynyl-derivatized cap analog refers to an extendible di-nucleotidecap, containing an alkynyl group at a 2′ or 3′ position, thatfacilitates transcription of a template, translation of a transcript,and/or confers stability to an RNA transcript. The cap analog isincorporated at the 5′ end of an RNA transcript. Examples ofalkynyl-derivatized cap analogs are provided by FIG. 1A-FIG. 1L in whichan alkynyl moiety is attached at the 3′ or 2′ position on the ribosering as designated, for example, by the structure: R₃^(7,3′-O-alkynyl)G[5′]p[p]_(n)p[5′]R₄ ⁷G, or R₃^(7,2′-O-alkynyl)G[5′]p[p]_(n)p[5′]R₄ ⁷G.

For some alkynyl-derivatized cap analogs having the structure:

R₃ and R₄ may be alkyl or arylalkyl. In some embodiments, the alkyl ismethyl, ethyl, propyl, isopropyl, butyl or isobutyl. In otherembodiments, the alkyl is methyl, ethyl, propyl or butyl. In someembodiments, the alkyl is a C1 to C12 alkyl. Representative examples ofalkyl groups include methyl, ethyl, straight-chain, branched or cyclicisomers of propyl, butyl, pentyl, hexyl, heptyl, octyl, nonyl, anddecyl. Alkyl groups may be substituted by at least one functional group.An arylalkyl group may be a moiety having a ring structurecharacteristic of benzene, naphthalene, phenanthrene, anthracene, andthe like, i.e., either the 6-carbon ring of benzene or the condensed6-carbon rings of the other aromatic derivatives. For example, an arylgroup may be phenyl or naphthyl, and the term as used herein includesboth unsubstituted aryls and substituted aryls.

A salt of an alkynyl-derivatized cap analog comprises a physiologicallyacceptable salt, such as a monovalent salt, for example, TEA, Tris, Li+,Na+ or ammonium, for example.

Alkynyl-derivatized cap analogs can be synthesized using the methodshown in FIG. 2 where monophosphorylation of 3′-O-propargyl guanosine 1was achieved using POCl₃ and trimethyl phosphate and resulted in3′-O-propargyl GMP 2. The imidazolide reaction of 2 with imidazole,triphenyl phosphine, and aldrithiol resulted in the correspondingimidazolide salt, 3′-O-propargyl ImGMP 3. Next, the resultingimidazolide salt 3 was further phosphorylated using (Bu₃NH)₃PO₄ in thepresence of zinc chloride as the catalyst and resulted in 3′-O-propargylGDP 4. The methylation of 4 using dimethyl sulfate as the methylatingagent under acidic conditions resulted in a highly regioselective N7methylation product 5. Finally, the coupling reaction ofm^(7,3′-O-propargyl)GDP 5 with ImGMP 6 in the presence of zinc chlorideas the catalyst resulted in m^(7,3′-O-propargyl)G[5′]ppp[5′]G 7.

The term “alkynyl-modified capped RNA” refers to RNA having analkynyl-derivatized cap covalently bonded thereto. In some embodiments,the RNA is mRNA. In other embodiments, the RNA is non-coding RNA.

Reaction of an alkynyl-derivatized capped RNA with an azide˜cleavablelinker˜reporter molecule/solid support yields a 1,4-disubstitutedtriazole-derivatized capped RNA˜cleavable linker˜reporter molecule/solidsupport conjugate. Cleavage of the linker results in a 1, 4-substitutedtriazole-derivatized capped RNA˜linker conjugate. The structure of thecleaved product varies depending on the structure of the linker and themethod of cleavage. For example, cleavage of a linker containing adisulfide bond yields a sulfhydryl group at the end of the linker.

A linker can be a moiety that attaches a reporter or a solid support toalkynyl-derivatized capped RNA, which linker is cleavable underconditions that minimize damage to RNA. Alternatively, a linker canattach alkynyl-derivatized capped RNA to a solid support without the useof a reporter. The attachment is via the alkyne group on thealkynyl-derivatized capped RNA and an azide group on the reporter or thesolid support.

A linker can be a cleavable linker. A “cleavable linker” is a linkerthat has one or more cleavable groups that may be broken by the resultof a reaction or condition. The term “cleavable group” refers to amoiety that allows for release of a portion, e.g., a reporter moiety,carrier molecule or solid support, of a conjugate from the remainder ofthe conjugate by cleaving a bond linking the released moiety to theremainder of the conjugate. Such cleavage is either chemical in nature,or enzymatically mediated. Exemplary enzymatically cleavable groupsinclude natural amino acids or peptide sequences that end with a naturalamino acid. In addition to enzymatically cleavable groups, it is withinthe scope of the present invention to include one or more sites that arecleaved by the action of an agent other than an enzyme. Exemplarynon-enzymatic cleavage agents include, but are not limited to, reducingagents (i.e., DTT or mercaptoethanol), acids, bases, light (e.g.,nitrobenzyl derivatives, phenacyl groups, benzoin esters), heat, as wellas other cleavable groups known in the art. Moreover a broad range ofcleavable, bifunctional (both homo- and hetero-bifunctional) spacer armsare commercially available. An exemplary cleavable group, an ester, iscleavable group that may be cleaved by a reagent, e.g. sodium hydroxide,resulting in a carboxylate-containing fragment and a hydroxyl-containingproduct. Exemplary cleavable linkers include disulfide bonds andPC-linkers. Other linkers are discussed in the art, including U.S. Pat.No. 7,572,908, herein incorporated by reference in its entirety. Alinker which has a disulfide linkage (S—S) can be cleaved by usingdithiothreitol, e.g., a 50 mM solution of DTT. A linker which hasphotocleavable linkers (PC-Linkers) can be cleaved with certain UVlights.

The term “solid support,” as used herein, refers to a material that issubstantially insoluble in a selected solvent system, or which can bereadily separated from a selected solvent system in which it is soluble.Solid supports useful in practicing the methods herein can includegroups that are activated or capable of activation to allow selected oneor more compounds described herein to be bound to the solid support. Thematerial in the solid support may include a mineral or polymer, in whichcase the support is referred to as a “mineral or polymer support.”Mineral or polymer supports include supports involving silica. In someembodiments, the silica is glass. Supports include, but are not limitedto, beads, magnetic beads, columns and filters. In further embodiments,the mineral or polymer support is a glass fiber filter or column. Insome embodiments, affinity chromatography can be used to isolate thecapped and derivatized mRNAs from the uncapped mRNAs.

The term “reporter moiety” and “reporter” are interchangeable and referto a moiety that is detectable. In some embodiments, the reporter isspecifically bound by an affinity moiety. In some embodiments, theinteraction of the reporter moiety and the affinity moiety provides forthe isolation of 1,4-triazole-derivatized RNA that is attached to thereporter moiety. Examples include, but are not limited to biotin oriminobiotin and avidin or streptavidin. A sub-class of reporter moietyis an “epitope tag,” which refers to a tag that is recognized andspecifically bound by an antibody or an antigen-binding fragmentthereof. Other reporters include, but are not limited to tags (withaffinity partner), epitope tags (with antibody), and enzyme substrate(with enzyme). The reporter moiety can allow for attachment to a solidsupport for purification of the capped RNA. The reporter can be, forexample, a dye, biotin, or a peptide. Examples of biotin molecules thatcan comprise the reporter moiety include C₅-C₂₀ O-biotin, SS-biotin,XX-biotin ((6-((6-((biotinoyl)amino)hexanoyl)amino)hexanoic acidsuccinimidyl ester), and NHS esters. For use in certain methods herein,the reporter includes an azide group to allow use in “click” technology.

Alkynyl-derivatized cap analogs provided herein are used for thesynthesis of 5′ alkynyl-derivatized capped RNA molecules in in vitrotranscription reactions. Substitution of alkynyl-derivatized cap analogsfor a portion of the GTP in a transcription reaction results in theincorporation of the alkynyl-derivatized cap structure into acorresponding fraction of the transcripts.

Alkynyl-derivatized capped mRNAs are generally translated moreefficiently in reticulocyte lysate and wheat germ in vitro and in vivotranslation systems as compared to standard capped mRNA. As provided byExample 4 below, luciferase activity was measured and revealed that theprotein production using alkynyl-derivatized capped mRNA 7 (FIG. 2) wasup to 3 fold higher than that using the standard cap (m⁷GpppG-capped)mRNA (FIG. 6).

Embodiments herein provide for methods of using alkynyl-derivatized capanalogs to isolate mRNAs encoding specific genes to be transfected intoeukaryotic cells or microinjected into cells or embryos to study theeffect of translated product in the cell or embryo. Also included aremethods of treating disease by transfecting such isolated mRNAs intocells isolated from a patient and thus expressing the specific proteinencoded by the mRNAs.

The term “antigen presenting cell” (APC) refers to a cell displaying anantigen-MHC complex on its surface. The T-cell receptor of T-cells mayrecognize the antigen. Examples of APCs include without limitationdendritic cells, macrophages, B-cells, fibroblasts (skin), thymicepithelial cells, thyroid epithelial cells, glial cells (brain),pancreatic beta cells, and vascular endothelial cells (Steinman, R. M.and J. Banchereau, Nature 449, 419-426 (2007)) incorporated herein byreference).

Alkyne-derivatized cap analogs and, in particular, RNA coupled to analkyne-derivatized cap analog, are/is detected or isolated by couplingthe alkyne portion with an azide-derivatized reporter moiety, forexample for detection, or an azide derivatized solid support forisolation, for example.

Azides and terminal alkynes undergo copper(I)-catalyzed azide-alkynecycloaddition at room temperature. Such copper(I)-catalyzed azide-alkynecycloadditions, also known as “click” chemistry, is a variant of theHuisgen 1,3-dipolar cycloaddition wherein organic azides and terminalalkynes react to give 1,4-disubstituted 1,2,3-triazoles. Examples of“click” chemistry reactions are described by Sharpless et al. U.S.Patent Application Publication No. 20050222427, published Oct. 6, 2005,PCT/US03/17311, U.S. Pat. Nos. 7,375,234 and 7,763,736 (whichpublications are herein incorporated by reference in their entirety);Lewis W G, et al., Angewandte Chemie-Infl Ed, 41:6, 1053; methodreviewed in Kolb, H. C., et al, Angew. Chem. Inst. Ed. 2001, 40,2004-2021, which developed reagents that react with each other in highyield and with few side reactions in a heteroatom linkage (as opposed tocarbon-carbon bonds) in order to create libraries of chemical compounds.

The copper used as a catalyst for the “click” reaction used in somemethod embodiments described herein is in the Cu (I) reduction state.The sources of copper(I) used in such copper(I)-catalyzed azide-alkynecycloadditions can be any cuprous salt including, but not limited to,cuprous halides such as cuprous bromide or cuprous iodide. However, thisregioselective cycloaddition can also be conducted in the presence of ametal catalyst and a reducing agent. In certain embodiments, copper canbe provided in the Cu (II) reduction state, for example, as a salt, suchas but not limited to Cu(NOs)₂ Cu(OAc)₂ or CuSO₄, in the presence of areducing agent wherein Cu(I) is formed in situ by the reduction ofCu(II). Such reducing agents include, but are not limited to, ascorbate,tris(2-carboxyethyl) phosphine (TCEP), 2,4,6-trichlorophenol (TCP),NADH, NADPH, thiosulfate, metallic copper, quinone, hydroquinone,vitamin K₁, glutathione, cysteine, 2-mercaptoethanol, dithiothreitol,Fe²⁺, Co²⁺, or an applied electric potential. In other embodiments, thereducing agents include metals selected from Al, Be, Co, Cr, Fe, Mg, Mn,Ni, Zn, Au, Ag, Hg, Cd, Zr, Ru, Fe, Co, Pt, Pd, Ni, Rh, and W.

The copper(I)-catalyzed azide-alkyne cycloadditions can be performed inwater, an aqueous solution of a variety of solvents, including mixturesof water and (partially) miscible organic solvents including alcohols,dimethyl sulfoxide (DMSO), dimethyl formamide (DMF), tert-butanol(tBuOH) and acetone, or in organic solvents such as tetrahydrofuran.

Without limitation to any particular mechanism, copper in the Cu (I)state is a preferred catalyst for the copper(I)-catalyzed azide-alkynecycloadditions, or “click” chemistry reactions, used in the methodsdescribed herein. Certain metal ions are unstable in aqueous solvents,by way of example Cu(I), therefore stabilizing ligands/chelators can beused to improve the reaction. In certain embodiments at least one copperchelator is used in the methods described herein, wherein such chelatorsbinds copper in the Cu (I) state. In certain embodiments at least onecopper chelator is used in the methods described herein, wherein suchchelators binds copper in the Cu (II) state. In certain embodiments, thecopper (I) chelator is a 1,10 phenanthro line-containing copper (I)chelator. Non-limiting examples of such phenanthro line-containingcopper (I) chelators include, but are not limited to,bathophenanthroline disulfonic acid (4,7-diphenyl-1,10-phenanthrolinedisulfonic acid) and bathocuproine disulfonic acid (BCS;2,9-dimethyl-4,7-diphenyl-1,10-phenanthroline disulfonate). Otherchelators used in such methods include, but are not limited to,N-(2-acetamido)iminodiacetic acid (ADA), pyridine-2,6-dicarboxylic acid(PDA), S-carboxymethyl-L-cysteine (SCMC), trientine,tetra-ethylenepolyamine (TEPA),NNNN-tetrakis(2-pyridylmethyl)ethylenediamine (TPEN), EDTA, neocuproine,N-(2-acetamido)iminodiacetic acid (ADA), pyridine-2,6-dicarboxylic acid(PDA), S-carboxymethyl-L-cysteine (SCMC),tris-(benzyl-triazolylmethyl)amine (TBTA), or a derivative thereof. Mostmetal chelators, a wide variety of which are known in the chemical,biochemical, and medical arts, are known to chelate several metals, andthus metal chelators in general can be tested for their function in 1,3cycloaddition reactions catalyzed by copper. In certain embodiments,histidine is used as a chelator, while in other embodiments glutathioneis used as a chelator and a reducing agent.

The concentration of the reducing agents used in the “click” chemistryreaction described herein can be in the micromolar to millimolar range.In certain embodiments the concentration of the reducing agent is fromabout 100 micromolar to about 100 millimolar. In other embodiments theconcentration of the reducing agent is from about 10 micromolar to about10 millimolar. In other embodiments the concentration of the reducingagent is from about 1 micromolar to about 1 millimolar.

In certain embodiments, in the methods described herein using “click”chemistry, at least one copper chelator is added after copper(II) usedin the reaction has been contacted with a reducing agent. In otherembodiments, at least one copper chelator can be added immediately aftercontacting copper(II) with a reducing agent. In other embodiments, thecopper chelator(s) is added between about five seconds and abouttwenty-four hours after copper(II) and a reducing agent have beencombined in a reaction mixture. In other embodiments, at least onecopper chelator can be added any time to a reaction mixture thatincludes copper(II) and a reducing agent, such as, by way of exampleonly, immediately after contacting copper(II) and a reducing agent, orwithin about five minutes of contacting copper(II) and a reducing agentin the reaction mixture. In some embodiments, at least one copperchelator can be added between about five seconds and about one hour,between about one minute and about thirty minutes, between about fiveminutes and about one hour, between about thirty minutes and about twohours, between about one hour and about twenty-four hours, between aboutone hour and about five hours, between about two hours and about eighthours, after copper(II) and a reducing agent have been combined for usein a reaction mixture.

In other embodiments, one or more copper chelators can be added morethan once to such “click” chemistry reactions. In embodiments in whichmore than one copper chelator is added to a reaction, two or more of thecopper chelators can bind copper in the Cu (I) state or, one or more ofthe copper chelators can bind copper in the Cu (I) state and one or moreadditional chelators can bind copper in the Cu (II) state. In certainembodiments, one or more copper chelators can be added after the initialaddition of a copper chelator to the “click” chemistry reaction. Incertain embodiments, the one or more copper chelators added after theinitial addition of a copper chelator to the reaction can be the same ordifferent from a copper chelator added at an earlier time to thereaction.

The concentration of a copper chelator used in the “click” chemistryreaction described herein can be determined and optimized using methodswell known in the art, including those disclosed herein using “click”chemistry to label nucleic acids followed by detecting such labelednucleic acids to determine the efficiency of the labeling reaction andthe integrity of the labeled nucleic acid(s). In certain embodiments,the chelator concentrations used in the methods described herein is inthe micromolar to millimolar range, by way of example only, from 1micromolar to 100 millimolar. In certain embodiments the chelatorconcentration is from about 10 micromolar to about 10 millimolar. Inother embodiments the chelator concentration is from about 50 micromolarto about 10 millimolar. In other embodiments the chelator, can beprovided in a solution that includes a water miscible solvent such as,alcohols, dimethyl sulfoxide (DMSO), dimethyl formamide (DMF),tert-butanol (tBuOH) and acetone. In other embodiments the chelator, canbe provided in a solution that includes a solvent such as, for example,tetrahydrofuran, dimethyl sulfoxide (DMSO) or dimethylformamide (DMF).

While the methods used herein involve a copper catalyzed covalentreaction between an alkyne and an azide, it is envisioned that othermethods using other catalysts (such as those using ruthenium) can alsobe used.

The “click” technology, as used herein, can result in isolation of up to100% of capped mRNA. In some embodiments, the method can be used toisolate capped RNA to 80% to 100% purity, including but not limited to,85%, 90%, 95%, and 100% purity. For example, 80% pure means that mRNAisolated using the “click” method results in less than 20% uncappedmRNA.

The scheme provided by FIG. 3 shows coupling of a RNA bearing analkyne-modified cap analog to an entity bearing an azide group using“click” chemistry. In this case, the azide bearing entity contains areporter moiety. In the presence of copper, a 1,4-disubstituted triazolederivative is formed containing capped RNA and the reporter. Thisconjugate, when contacted with an affinity column bearing an affinitymolecule that binds to the reporter, allows for isolation of the RNA.When the RNA is mRNA, the derivatized mRNA can then be used in vitro ina cellular translation assay to produce a protein of interest. Incertain embodiments, a reporter is not used and the alkynyl-modifiedcapped mRNA binds directly to an azide-derivatized solid support.

As shown in FIG. 5A and FIG. 5B, in the presence of THF and CuI, thealkynyl-modified capped mRNA 7 a binds to the azide derivatized solidsupport 10 a or 10 b, respectively. After washing, the solid supportedconjugates 11 a and 11 b are cleaved with DTT to yield the1,4-disubstituted triazole derivatives 12 a and 12 b, respectively.

The scheme of FIG. 7 provides for binding of alkyne-derivatized cappedmRNA 7 a to biotin 13 via a disulfide cleavable linkage. The resulting1,4-derivatized triazole conjugate 14 can be detected or, alternatively,detected and isolated using an affinity column bearing an avidin moietythat binds to the biotin to isolate the derivatized mRNA. Thederivatized mRNA can be cleaved by cleaving the disulfide (S—S) bond ofthe biotin (e.g., using DTT). The resultant mRNA can then be used invitro in a cellular translation assay to produce a protein of interest.

FIG. 8A and FIG. 8B provide azide containing cleavable linkersconjugated to a solid support or a reporter, 10 a and 10 b, for example.The solid support or reporter may have an amino moiety (9 a) forreaction with an ester (8 a) or a carboxy moiety (9 b) for reaction withan amine (8 b). Such linked solid supports or reporters can be used inmethods herein for binding to alkyne-derivatized cap analogs or toalkyne-modified capped RNA. In one embodiment of FIG. 8A, asolid-supported S—S linker with an azide group 10 a is produced byadmixing a linker structure having a disulfide linker bearing an azideon one end and an ester on the other 8 a with a solid support (e.g., abead) bearing an amino group 9 a in the presence of sodium bicarbonateas the base and THF as the solvent.

Cap analogs are used for the synthesis of 5′ capped RNA molecules intranscription reactions. Substitution of cap analog for a portion of theGTP in a transcription reaction results in the incorporation of the capstructure into a corresponding fraction of the transcripts.

Transcription of RNA usually starts with a nucleoside triphosphate(usually a purine, A or G). When transcription occurs in vitro, ittypically includes a phage RNA polymerase such as T7, T3 or SP6, a DNAtemplate containing a phage polymerase promoter, nucleotides (ATP, GTP,CTP and UTP) and a buffer containing magnesium salt. The synthesis ofcapped RNA includes the incorporation of a cap (e.g., m⁷GpppG) or a capanalog (such as those described herein) in the transcription reaction.Excess cap to GTP (e.g., 4:1) increases the opportunity that eachtranscript will have a 5′ cap. The mMESSAGE mMACHINE® kit from Ambion(Ambion, Inc., Austin, Tex., a business of Applied Biosystems)recommends this ratio and will typically yield 80% capped RNA to 20%uncapped RNA, although total yields of total RNA are lower as GTPconcentration becomes rate limiting as GTP is necessary for theelongation of the transcript.

In the scheme provided by FIG. 4, a flow chart for in vitrotranscription in the presence of an alkynyl-modified cap analog isprovided. Coupling of the alkyne-derivatized capped RNA via “click”chemistry to an azide-derivatized solid support containing a disulfidelinker provides for isolation of triazole-derivatized capped RNA. Thebead structure depicts a solid support or biotin or a reporter or apeptide. Uncapped RNA will not undergo the “click” reaction due to lackof an alkynyl-derivatized cap. After binding to the solid support, forexample, the supernatant can be washed off or filtration can beperformed to remove the uncapped RNA. The solid support with bound5′-triazole-derivatized capped RNA can be washed and the RNA cleavedfrom the solid support with a substance that cleaves the cleavablelinker (e.g., DTT for a disulfide). The cleaved 5′-triazole-derivatizedRNAs can then be filtered and subjected to ethanol precipitation.Precipitated material will contain only 5′-capped RNA, and when the RNAis mRNA, the mRNA is ready for a translation assay (FIG. 4). Thestructure of the isolated RNA would vary depending on the linker,position and type of cleavable group.

Capped mRNAs are generally translated more efficiently in reticulocytelysate and wheat germ in vitro translation systems. It is important thatin vitro transcripts be capped for microinjection experiments becauseuncapped mRNAs are rapidly degraded. Cap analogs are also used as ahighly specific inhibitor of the initiation step of protein synthesis.

The 5′ cap structure enhances the translation of mRNA by helping to bindthe eukaryotic ribosome and assuring recognition of the proper AUGinitiator codon. This function may vary with the translation system andwith the specific mRNA being synthesized. The consensus sequence5′-GCCACCAUGG-3′, also known as the “Kozak” sequence, is considered tobe the strongest ribosomal binding signal in eukaryotic mRNA. Forefficient translation initiation, the key elements are the 5′ G residueat the +1 position and the A residue at the 3′ position of the mRNA.

The mRNA can be transfected into a cell to be translatedintracellularly. Methods of transfection are known to those of skill inthe art and include microinjection, electroporation, chemical treatmentsand the like. Cells for use in in vivo translation include any patientcell for which it is desired to express a protein of interest. Cellsinclude hematopoietic cells (e.g., T cells, dendritic cells,macrophages, etc.), bone marrow cells, tissue culture cells, germ cells,and the like.

Compositions comprising alkynyl-modified capped RNA as described hereincan be used for in vitro transcription, in vitro translation, and invivo translation, for example. Current biotechnology efforts for invitro, in cyto, and in vivo protein production will also benefit fromthese methods and compositions. Further, compositions provided hereinare useful for therapeutic purposes. For example, the present technologymay be useful for generating vaccines against infectious diseases orcancers. Alkyne-derivatized capped RNA can be used to producenon-infectious particles of Venezuelan Equine Encephalitis viruscontaining an RNA encoding immunogen. These non-replicating viralparticles can be injected into humans where they can enter host cells.Once in the host cell, the viral particles dissociate and the mRNAencoding the immunogen is translated into protein. These proteins caninduce an immune response. These types of vaccines are expected to beuseful for human immunodeficiency virus (HIV), feline immunodeficiencyvirus, human papilloma virus type 16, tumors, lassa virus, Ebola virus,Marburg virus, anthrax toxin from Bacillus anthraces, and botulinumtoxin. These vaccine strategies can require large quantities of cappedRNA. The present methods facilitate such synthesis and subsequentpurification of capped RNA so as to make these vaccines commerciallyfeasible. As well, strategies to increase the percentage of full lengthcapped RNA in a transcription reaction leading to a more homogenousproduct will be preferred in the vaccine industry as highly purecomponents are usually required for human use. In addition, researchersprefer to use products that are as pure as possible to minimize thenumber of variables in an experiment. As well, the purer the product,the more potent it is.

Another use of compositions described herein involves isolatingdendritic cells (DCs) from a patient and then transfecting the dendriticcells with derivatized capped RNA as described herein encodingimmunogen. The dendritic cells translate the derivatized capped RNA intoat least one protein that induces an immune response against thisprotein.

In a small human study, immunotherapy with dendritic cells loaded withCEA capped RNA was shown to be safe and feasible for pancreatic cancerpatients (Morse et al., Int. J. Gastrointest. Cancer, 32, 1-6 (2002)).It was also noted that introducing at least one single capped RNAspecies into immature dendritic cells induced a specific T-cell response(Heiser et al., J. Clin. Invest, 109, 409-417 (2002)). The cap analogsprovided herein can be used for providing mRNAs for antigen delivery toDCs for the purpose of immunotherapy against cancer and infectiousdiseases.

Other uses include reprogramming differentiated cells to pluripotencyand/or to re-program pluripotent cells using capped RNA described hereinto specifically differentiate cell types by continuous transfection ofspecific derivatized-capped mRNAs over a time-period necessary forchanging the cell differentiation.

The 1,4-disubstituted triazole derivatized capped RNA is expected toassociate with biological targets through hydrogen bonding and dipoleinteractions that may play an important role in a drug discoveryprogram. For example, the triazole product contains three nitrogen atomsin the ring that are capable of hydrogen bonding with biologicaltargets.

An additional embodiment relates to the administration of a compositionwhich generally comprises an active ingredient (e.g., alkynyl-modifiedcapped RNAs or 1,4-disubstituted triazole capped RNAs) formulated with apharmaceutically acceptable excipient. Excipients may include, forexample, sugars, starches, celluloses, gums, and proteins. Variousformulations are commonly known and are thoroughly discussed in thelatest edition of Remington's Pharmaceutical Sciences (Maack Publishing,Easton Pa.). Such compositions may include novel cap analogs, antibodiesto novel cap analogs, and mimetics, agonists, antagonists, or inhibitorsof novel cap analogs.

In various embodiments, the compositions described herein, such aspharmaceutical compositions, may be administered by any number of routesincluding, but not limited to, oral, intravenous, intramuscular,intra-arterial, intramedullary, intrathecal, intraventricular,pulmonary, transdermal, subcutaneous, intraperitoneal, intranasal,enteral, topical, sublingual, or rectal means.

Embodiments of the present disclosure can be further understood in lightof the following examples, which should not be construed as limiting thescope of the present disclosure in any way.

EXAMPLES

The following examples provide methods of producing alkynyl-derivatizedcap analogs, alkynyl-modified capped RNA, 1,4-disubstitutedtriazole-derivatized capped RNA, as well as methods of isolation, anduses thereof.

Reagents:

Reagents and solvents are used as such without further purification,unless otherwise stated. 3′-O-propargyl guanosine was purchased fromChemgenes, USA, ¹H NMR and ³¹P NMR spectra were recorded in D₂O on aBurker 400 MHz instrument. ESI mass spectra were recorded on an AppliedBiosystems/Sciex API 150 model. HPLC was run on a waters 2996 (WatersCorporation) using anion exchange column. Ion exchange chromatographywas performed in an AKTA purifier (Amersham Biosciences, GE Healthcare)using a DEAE Sepharose column. The gel shift assay was performed byusing a pTri β actin template and the IVT reaction used linearizedAmbLuc poly(A) DNA template and a MEGASCRIPT kit (Life TechnologiesCorporation). Radiation in the gel bands of interest was quantified by aphosphorimager (GE Healthcare). Purifications of the RNA from thesetranscription reactions were done by using the MEGACLEAR Kit (LifeTechnologies Corporation) as per manufacturer's protocol. Luminometer(POLARstar OPTIMA. BMG Labtech) in 96-well plates was used for theluciferase assay readings as per manufacturer's protocol.

Example 1 Synthesis of Alkynyl-Derivatized Cap Analog

An exemplary alkynyl-derivatized cap analog of FIG. 1G was synthesizedusing the scheme shown in FIG. 2. Bold numbers 1-7 designate structures1-7 in FIG. 2. In brief, the monophosphorylation reaction of3′-O-propargyl guanosine 1 was achieved using POCl₃ and trimethylphosphate that furnished the corresponding 3′-O-propargyl GMP 2 in 85%yield. The imidazolide reaction of 2 with imidazole, triphenylphosphine, and aldrithiol furnished the corresponding imidazolide salt,3′-O-propargyl ImGMP 3 in 89% yield. Next, the resulting imidazolidesalt 3 was further phosphorylated using (Bu₃NH)₃PO₄ in the presence ofzinc chloride as the catalyst that furnished the corresponding3′-O-propargyl GDP 4 in 71% yield. Notably, the methylation of 4 usingdimethyl sulfate as the methylating agent under acidic conditionsfurnished a highly regioselective N7 methylation product 5 in 71% yield.Finally, the coupling reaction of m^(7,3′-O-propargyl)GDP 5 with ImGMP 6in the presence of zinc chloride as the catalyst furnishedm^(7,3′-O-propargyl)G[5′]ppp[5′]G 7 in 64% yield. Details are asfollows.

Synthesis of 3′-O-propargyl GMP 2:

To a stirred solution of POCl₃ (1.83 g, 12.12 mmol) and (MeO)₃PO (25.0mL) at 0° C. under an argon atmosphere, 3′-O-propargyl guanosine 1 (1.10g, 4.05 mmol) was added and the reaction mixture was stirred for 4 h at0° C. After 4 h, 50.0 mL water was added to the reaction mixture. Theresulting reaction mixture was washed with dichloro methane (2×50 mL) toremove the phosphorylating agent. The collected aqueous solution wasadjusted to pH 1.5 and allowed to stir at 4° C. for 15 h. After 15 h,the aqueous solution was adjusted to pH 6.5 and loaded on a DEAESepharose column The desired product was eluted using a linear gradientof 0-1M TEAB (triethyl ammonium bicarbonate, pH 7.5) and the fractionscontaining the product were pooled, evaporated and dried in a vacuumdesiccator over phosphorous pentoxide to give a fine white powder 2(Yield: 1.70 g, 85%).

Synthesis of 3′-O-propargyl ImGMP 3:

To a stirred solution of 3′-O-propargyl GMP (1.50 g, 2.99 mmol) in 25 mLdry DMF, imidazole (0.97 g, 14.92 mmol), triphenyl phosphine (1.57 g,5.99 mmol), aldrithiol (1.32 g, 6.00 mmol) and triethylamine (0.30 g,2.97 mmol) were added. The reaction mixture was stirred under an argonatmosphere at room temperature for 16 h. To a solution of sodiumperchlorate (1.50 g) in 100 mL acetone in a centrifuge tube at 0° C.,the above reaction mixture was added slowly for 5 minutes. The resultingmixture was centrifuged and the supernatant liquid was removed. Thesolid was ground with a new portion of acetone (100 mL), cooled, andcentrifuged again. This process was repeated two more times, and theresulting solid was dried in a vacuum desiccator over P₂O₅ to give awhite powder 3 (Yield: 1.26 g, 89%).

Synthesis of 3′-O-propargyl GDP 4:

To a stirred solution of 3′-O-propargyl ImGMP 3 (1.20 g, 2.67 mmol) andzinc chloride (1.81 g, 13.30 mmol) in 10.0 mL dry DMF, 15 mL of 1Mtris(tributylammonium) phosphate in DMF was added under an argonatmosphere. The reaction mixture was stirred at room temperature for 5h. After 5 h, the reaction mixture was diluted with 50.0 mL of water.The resulting reaction mixture was washed with ethyl acetate (2×50 mL)to remove phosphorylating agent. The collected aqueous solution wasadjusted to pH 6.5 and loaded on a DEAE Sepharose column. The desiredproduct was eluted using a linear gradient of 0-1M TEAB and thefractions containing the product were pooled, evaporated and dried in avacuum desiccator over phosphorous pentoxide to give a fine white powder4 (Yield 1.29 g, 71%).

Synthesis of m^(7,3′-O-propargyl)GDP 5:

To a stirred solution of 3′-O-propargyl GDP 4 (1.10 g, 1.61 mmol) in20.0 mL of water, acetic acid was added slowly to adjust the pH of thesolution to 4.0. To this mixture, dimethyl sulfate (3.0 mL) was addeddrop-wise over a period of 30 min. and the reaction mixture was allowedto stir at room temperature for 5 h. As the methylation proceeded, thepH dropped down to around 2.0 and the pH was readjusted back to 4.0using 1M NaOH solution. After 5 h, the reaction mixture was extractedwith ethyl acetate (2×25 mL) to remove unreacted excess dimethylsulfate. The collected aqueous solution was adjusted to pH 6.5 andloaded on a DEAE Sepharose column. The desired product was eluted usinga linear gradient of 0-1M TEAB and the fractions containing the productwere pooled, evaporated and dried in vacuum desiccator over phosphorouspentoxide to give a fine white powder 1 (Yield 0.79 g, 71%).

Synthesis of Reactant ImGMP 6:

To a stirred solution of GMP TEA salt (5.00 g, 10.80 mmol) in 50 mL dryDMF, imidazole (3.51 g, 54.00 mmol), triphenyl phosphine (5.66 g, 21.60mmol), aldrithiol (4.75 g, 21.59 mmol) and triethylamine (1.10 g, 10.89mmol) were added. The reaction mixture was stirred under argonatmosphere at rt for 15 h. To a solution of sodium perchlorate (5.0 g)in 250 mL acetone in a centrifuge bottle at 0° C., the above reactionmixture was added slowly for 5 minutes. The resulting mixture wascentrifuged and the supernatant liquid was removed. The solid was groundwith a new portion of acetone (250 mL), cooled, and centrifuged again.This process was repeated for two more times, and the resulting solidwas dried in a vacuum desiccator over P₂O₅ to give a white powder 6(Yield: 4.46 g, 94%).

Synthesis of m^(7,3′-O-propargyl)G[5′]ppp[5′]G 7:

To a stirred solution of m^(7,3′-O-propargyl)GDP 5 (0.20 g, 0.29 mmol)and ImGMP 6 (0.12 g, 0.28 mmol) in 10.0 mL dry DMF, zinc chloride (0.19g, 1.40 mmol) was added under an argon atmosphere and the reactionmixture was stirred at room temperature for 60 h. After 60 h, thereaction mixture was added to a solution of EDTA disodium (0.52 g, 1.40mmol) in 100.0 mL of water at 0° C. The resulting aqueous solution wasadjusted to pH 6.5 and loaded on a DEAE Sepharose column. The desiredproduct was eluted using a linear gradient of 0-1M TEAB and thefractions containing the product were pooled, evaporated andconcentrated to 10.0 mL TEA salt of 7. The resulting 10.0 mL was passedthrough a Strata-X-AW column and washed with 10.0 mL water followed by10.0 mL MeOH. Then, the desired compound was eluted with 15.0 mL ofNH₄OH/MeOH/H₂O (Feb. 25, 1973) and the collected solution was evaporatedand dried to give a fine white powder 7. (Yield: 0.16 g, 64%).

Example 2 Analysis of Products by ¹H NMR and Mass Spectroscopy

The products from Example 1 were analyzed by ¹H NMR and MassSpectroscopy as follows: ¹H NMR and ³¹P NMR spectra were recorded in D₂Oon a Bruker 400 MHz instrument. ¹H was collected at 400.1446006 MHz andthe ³¹P was collected at 161.9968531, both using a QNP probe. Chemicalshifts are reported in ppm, and signals are described as s (singlet), d(doublet), t(triplet), q (quartet), and m (multiplet). ESI mass wasrecorded on a Applied Biosystems/Sciex MDX API 150 model.

Data for m^(7,3′-O-propargyl)G[5′]ppp[5′]G was as follows: ¹H NMR (D₂O,400 MHz) δ 7.99 (s, 1H), 5.87 (d, J=4.0 Hz, 1H), 5.79 (d, J=6.0 Hz, 1H),4.68 (m, 2H), 4.49-4.21 (m, 10H), 4.06 (s, 3H), 2.91 (t, J=2.2 Hz, 1H);³¹P NMR (D₂O, 162 MHz) δ −10.23 (d, J=20.7 Hz, 1P), −10.52 (d, J=19.4Hz, 1P), −21.88 (t, J=20.1 Hz, 1P); MS (m/z): 839 [M+H]⁺. The resultsshow that the expected chemical structure 7 was obtained.

Example 3 Transcriptional Capping Efficiency of Standard vsAlkyne-Derivatized CAP Analog

The capping efficiencies of standard cap analog (Ambion, LifeTechnologies Corp.) and alkyne-derivatized CAP analog 7 (see Example 1)were tested using the following transcription and translation tests (seeExample 4 for the translation test).

To analyze capping efficiency during transcription a Gel Shift Assay wasused. The Gel shift assay was performed using the MAXISCRIPT kit (LifeTechnologies Corporation) by following the manufacturer's protocol. Atypical 20 μL T7 RNA polymerase transcription reaction contained thefollowing reagents at the final concentrations indicated: linearizedpTri β actin vector template, 0.5 μg; ATP, 2 mM; GTP, 0.4 mM; compoundstandard cap analog and alkynyl-derivatized cap analog 7, 1.6 mM each inseparate reactions; 10× reaction buffer, 4 μl; T7 RNA polymerase, 50units/μL; (α-³²P) ATP, 800 (Ci/mmol); and DEPC water. The controlreaction was a normal in vitro transcription reaction, in which no capanalog was added. The transcription reactions were incubated at 37° C.for 2 h, after which the reaction mixtures were then applied to a 20%dPAGE gel. Radiation in the gel bands of interest was quantified by aphosphoroimager (GE Healthcare).

Due to the omission of CTP and UTP, only the 5′ end was transcribed byT7 RNA polymerase, producing a transcript of six nucleotides in length.The resulting transcription products were analyzed by 20% denaturingpolyacrylamide/8 M urea gel. The results from the gel shift assay showedthat the standard cap had a capping efficiency of 73% while thealkynyl-derivatized cap analog 7 had a capping efficiency of 60%.

Example 4 Translation Efficiency of Standard vs Alkyne-Derivatized CAPAnalog

Alkynyl-derivatized capped mRNAs were produced in vitro for use intranslation assays. T7 RNA polymerase transcription was performed usingthe MEGASCRIPT kit (Ambion, Life Technologies Corp.) in 20 μL finalvolume; the reaction contained the following reagents at the finalconcentrations indicated: linearized AmbLuc poly(A) DNA, 1.5 μg;1×reaction buffer; ATP, UTP, and CTP, 7.5 mM each; GTP, 1.5 mM;alkynyl-modified cap analog 7 or m⁷GpppG cap analog, 6.0 mM; and 50units/μl of T7 RNA polymerase. The transcription reactions wereincubated at 37° C. for 2 h. In order to hydrolyze the remaining plasmidDNA, 1 μL of TURBO DNase was added to the reaction mixture and furtherincubated at 37° C. for 15 min. Purification of transcription reactionswas done by using the MEGAclear™ kit (Life Technologies Corp) as permanufacturer's protocol. The in vitro transcription results in a mixtureof 5′ analog-capped and uncapped mRNAs.

To determine the translational efficiency, the luciferase mRNA poly(A)product generated from the transcription reaction using a standard capand the luciferase mRNA poly(A) product generated as described aboveusing the alkyne-derivatized cap 7 were transfected separately into HeLacells.

The HeLa cells (60,000/well in 24 well-plates) were seeded at least 12 hbefore transfection in growth medium without antibiotics. Capped RNA wasprepared by mixing 600 ng of RNA, 2.5 μL of TFX-20™ (Promega), and 300μL of serum-free DMEM in polystyrene tubes and incubated for 15 min atroom temperature. After the incubation, media from the pre-plated HeLacells was removed and 200 μL of the complex was added to each well. Theplates were incubated for 1 h at 37° C., and then 1 mL of pre-warmedmedia with serum was added. The transfected plates were incubated at 37°C. for 16 h. Cells were harvested and lysed after 16 h. The cells wereharvested by removing the media and adding 100 μL of 1× passive lysisbuffer (Promega). The plate was mixed carefully to disrupt the cells and10 μL of cell lysates from each transfection reactions were mixed with100 μL of luciferase substrate (Promega) and measured immediately on aPOLARstar OPTIMA Luminometer (BMG Labtech) in 96-well plates. The foldinduction of luciferase protein data was normalized to the controlreaction, i.e. no cap, mRNA poly(A) transfection results.

The translational luciferase data are provided in FIG. 6. The datareveal that the signal from protein produced from the luceriferase mRNAhaving alkyne-derivatized cap analog 7 a was 3.1-fold greater than frommRNA having the standard cap analog. This result is comparable to thetranslational properties of the anti-reverse cap analogs of publishedU.S. Patent Appl'n No. 2010/0261231 published on Oct. 14, 2010.

Without being bound by theory, the translational properties of mRNAhaving alkyne-derivatized cap analog 7 a over mRNA having the standardanalog may be due to the formation of exclusive forward-capped mRNApoly(A) transcripts that lead to a homogeneous population of RNAmolecules and/or due to the presence of the 3′-O-propargyl group, whichmight add to the stability of mRNA to accelerate the overalltranslational efficiency.

An advantage of the alkyne-derivatized cap analog derivatized mRNA isthe ease of isolation of exclusively capped molecules as describedbelow.

Example 5 Isolation of Capped mRNA using the “Click” Reaction

In vitro transcription (IVT) results in 5′ capped and uncapped mRNAs asa mixture. Since only the 5′ capped mRNA has an alkynyl-derivatized cap,the capped molecules alone undergo the “click” reaction for purificationof the capped mRNA. The “click” reaction is performed by usingsolid-supported azides with or without a cleavable linker arm, or biotinazide derivatives with or without a cleavable linker arm, or anyreporter moiety derivatized with azide (e.g., dyes, heptanes) with orwithout a cleavable linker. The “click” reaction of the azide derivativeand mRNA capped with an alkynyl-derivatized cap analog is performed inthe presence of copper and tetrahydrofuran (THF). The reaction resultsin formation of a −1,2,3 triazole linker-mRNA product, while uncappedmRNA does not undergo the “click” reaction. The supernatant is thenwashed off or filtration is performed, so that the uncapped mRNA (thatdid not bind to the solid support) is washed away. The solid supporthaving the bound 5′ capped mRNA is washed three times with water (or upto ten times) and cleaved from the solid support (using TNF). Cleaved5′capped mRNAs are filtered and subjected to ethanol precipitation.Precipitated material will contain only 5′ capped mRNAs, which are readyfor translation and/or transfection into a cell.

FIG. 5A and FIG. 5B provide schemes for isolation of 5′-capped mRNAusing alkynyl-derivatized cap analog technology involving asolid-supported azide having different cleavable linkers. In eachscheme, mRNA bearing an alkynyl-derivatized cap analog is admixed with asolid support bearing a cleavable linker and an azide group. In thepresence of copper and THF, the “click” product is formed. The resultingalkynyl-derivatized capped mRNA attached to the solid support is thenwashed to remove unbound mRNA. The capped mRNA is cleaved from the solidsupport using DTT. The resulting capped mRNA can then be used in vitroin a cellular translation assay to produce a protein of interest, forexample, or for in vivo use.

Example 6 Attachment of Derivatized Biotin to Alkynyl-Derivatized CapAnalog mRNA

FIG. 7 provides a scheme for coupling a mRNA having an alkynyl-modifiedcap analog 7 a with azido S—S-Biotin conjugate 13. Admixing in thepresence of copper and THF results in the “click” reaction to form S—SBiotin linked capped mRNA 14. The product is then run through anaffinity column bearing a streptavidin or avidin moiety which binds tothe biotin to isolate the capped mRNA (alternatively, it can be admixedwith magnetic beads bearing a streptavidin or avidin affinity moiety).The capped mRNA 14 is cleaved by cleaving the disulfide (S—S) bond ofthe biotin (e.g., using DTT). The capped mRNA can then be used in vitroin a cellular translation assay to produce a protein of interest.

Example 7 Preparation of Azide-Derivatized Solid-Supports having aCleavable Linker

In each of FIG. 8A and FIG. 8B, a scheme is provided in which anazide-derivatized solid-support having a cleavable disulfide linkage isproduced. For example, solid support 10 a of FIG. 8A is produced byadmixing a linker structure having a disulfide linker bearing an azideon one end and an ester on the other 8 a with a solid support (e.g., abead) bearing an amino group 9 a in the presence of sodium bicarbonateas the base and THF as the solvent. The resulting solid support havingan S—S linker and a terminal azide group can be used in methods of“click” chemistry to attach an alkynyl bearing capped mRNA. In oneembodiment, this method includes use of a reporter or affinity moiety.The “clicked” and capped mRNA can be cleaved from the solid support bycleaving the S—S bond.

Solid support 10 b of FIG. 8B is formed by reacting the amine of 8 bwith the carboxylated solid support 9 b. Again, the “clicked” and cappedmRNA can be cleaved from the solid support by cleaving the S—S bond.

Although the present disclosure is described with respect to certainembodiments and examples, various modifications may be made withoutdeparting from the spirit and scope of the invention.

1. A composition comprising an alkynyl-derivatized cap analog having thestructure: R₃ ^(7,3′-O-alkynyl)G[5′]p[p]np[5′]G, R₃^(7,3′-O-alkynyl)G[5′]p[p]np[5′]A, R₃ ^(7,2′-O-alkynyl)G[5′]p[p]np[5′]G,R₃ ^(7,2′-O-alkynyl)G[5′]p[p]np[5′]A, or a salt thereof, wherein R₃ isalkyl or arylalkyl, the alkynyl moiety comprises 3-24 carbon atoms, aterminal alkyne, and is optionally substituted, n is 1, 2, or 3, A isadenosine, and G is guanosine.
 2. A composition comprising RNA having acap analog of claim 1 covalently bonded thereto.
 3. A compositioncomprising an alkynyl-derivatized cap analog having the structure:

or a salt thereof, wherein at least one of R₁ and R₂ comprisesO(CH₂)_(m)C≡CH and m is 1 to 6, and the other of R₁ and R₂ comprises OHor H; R₃ is alkyl or arylalkyl; and R₄ is absent, H, alkyl or arylalkyl.4. The composition of claim 3, wherein R₂ comprises O(CH₂)_(m)C≡CH and mis 1 to 6, and R₁ comprises OH.
 5. The composition of claim 3, whereinR₁ comprises O(CH₂)_(m)C≡CH and m is 1 to 6, and R₂ comprises OH.
 6. Thecomposition of claim 4, wherein m is
 1. 7. The composition of claim 3wherein the alkyl is methyl, ethyl, propyl, isopropyl, butyl orisobutyl.
 8. The composition of claim 3 attached to the 5′ end of an RNAmolecule.
 9. The composition of claim 8 wherein the RNA molecule is amRNA molecule.
 10. A method of producing alkynyl-modified capped RNAcomprising: contacting a nucleic acid substrate with a RNA polymeraseand the alkynyl-derivatized cap analog of claim 3 in the presence ofnucleotide triphosphates under conditions and for a time to producealkynyl-modified capped RNA.
 11. The method of claim 10 furthercomprising contacting the alkynyl-modified capped RNA with anazide-derivatized moiety to form a 1,4-disubstitutedtriazole-derivatized capped RNA.
 12. The method of claim 11 wherein theazide-derivatized moiety comprises a detectable moiety.
 13. (canceled)14. The method of claim 12 wherein the method further comprisescontacting the 1,4-disubstituted triazole-derivatized capped RNA with asolid support having binding affinity and specificity for the detectablemoiety.
 15. (canceled)
 16. The method of claim 12 further comprisingdetecting the 1,4-disubstituted triazole-derivatized capped RNA.
 17. Amethod of separating alkynyl-modified capped RNA from uncapped RNA in asample, comprising: contacting the sample with a solid support having anazide-derivatized cleavable linker bound thereto under conditions andfor a time to produce a 1,4-disubstituted triazole-derivatized cappedRNA-solid support conjugate; separating the conjugate from uncapped RNA;and, cleaving the 1,4-disubstituted triazole-derivatized capped RNA fromthe solid support, thereby separating the alkynyl-modified capped RNAfrom uncapped RNA.
 18. (canceled)
 19. (canceled)
 20. A compositioncomprising a solid support having the structure:


21. A kit comprising: the alkynyl-derivatized cap analog of claim 3;nucleotide triphosphate molecules; and a RNA polymerase.
 22. (canceled)23. A biological cell comprising a 1,4-disubstitutedtriazole-derivatized capped RNA.
 24. A method of introducing anexogenous protein into a subject, comprising: transfecting the subjectwith a 1,4-disubstituted triazole-derivatized capped mRNA encoding theexogenous protein; and allowing intracellular translation to produce theexogenous protein.
 25. (canceled)
 26. (canceled)